--- /dev/null
+<HEAD>
+<TITLE> STEP 2 COMMANDS</TITLE>
+</HEAD>
+<BODY><P>
+ <HR> <A NAME=tex2html393 HREF=subsection3_16_2.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/next_motif.gif"></A> <A NAME=tex2html391 HREF=subsection3_16_1.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/up_motif.gif"></A> <A NAME=tex2html387 HREF=subsubsection3_16_1_3.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/previous_motif.gif"></A> <A NAME=tex2html395 HREF=tableofcontents3_1.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/contents_motif.gif"></A> <BR>
+<B> Next:</B> <A NAME=tex2html394 HREF=subsection3_16_2.html> AMPS Block file </A>
+<B>Up:</B> <A NAME=tex2html392 HREF=subsection3_16_1.html> ALSCRIPT Command Summary</A>
+<B> Previous:</B> <A NAME=tex2html388 HREF=subsubsection3_16_1_3.html> OPTIONAL STEP 1 </A>
+<HR> <P>
+<H3><A NAME=SECTION00016140000000000000> STEP 2 COMMANDS</A></H3>
+<P>
+All these are optional formatting commands.
+<P>
+IMPORTANT PLEASE READ THIS NOTE:
+<P>
+For those commands that accept region definitions (e.g. SURROUND_CHARS) it
+is easiest to think of the region being defined in terms of X and Y
+coordinates, where X is the sequence residue coordinate and Y is the
+sequence number coordinate. Thus 3 7 means the 3rd residue in sequence 7.
+3 7 12 42 means the rectangular box bounded by residue 3 of sequence 7 and
+residue 12 of sequence 42.
+<P>
+SURROUND_CHARS <string> ALL
+<P>
+Draw lines round, but not between the characters that are in the string.
+e.g.
+<P>
+SURROUND_CHARS GP ALL
+<P>
+will draw lines round all G and P characters in the alignment, but not
+between adjacent G and P characters.
+<P>
+SURROUND_CHARS <string> <int> <int> <int> <int>
+<P>
+Similar command, but the surrounding is restricted to the region defined by
+the four integers.
+<P>
+e.g.
+<P>
+SURROUND_CHARS ILVW 3 12 7 32
+<P>
+would surround ILVW characters that occur in the region defined
+from residue positions 3-7 of sequences 12 to 32.
+<P>
+SHADE_CHARS <string> ALL <float>
+<P>
+Shade all characters in the <string> by the grey value given by <float>.
+e.g.
+<P>
+SHADE_CHARS GP ALL 0.5
+<P>
+would shade all G and P characters in the alignment by the grey value 0.5.
+<P>
+SHADE_CHARS <string> <int> <int> <int> <int> <float>
+<P>
+restricts the shading to the region defined by the four integers. Thus
+<P>
+SHADE_CHARS ILVW 3 12 7 32 0.7
+<P>
+would shade I L V and W characters from residues 3-7 of sequences 12-32
+inclusive with a grey value of 0.7.
+<P>
+FONT_CHARS <string> ALL <int>
+<P>
+e.g.
+<P>
+FONT_CHARS GP ALL 7
+<P>
+would use font 7 to write out all G and P characters. Font 7 MUST have been
+defined using the DEFINE_FONTcommands above.
+<P>
+FONT_CHARS <string> <int> <int> <int> <int> <int>
+<P>
+Similar to previous command, but restricts the effect to the region defined
+by the first four integers. The font must have been defined by the
+DEFINE_FONT command.
+<P>
+e.g.
+<P>
+FONT_CHARS ILVW 3 45 9 70 7
+<P>
+Would set the font to 7 for I L V and W characters for residues 3-9 of
+sequences 45-70 inclusive. The font must have been defined by the
+DEFINE_FONT command.
+<P>
+FONT_REGION <int> <int> <int> <int> <int>
+<P>
+Define the font to use throughout the region specified by the first four
+integers.
+<P>
+e.g.
+<P>
+FONT_REGION 3 12 20 40 10
+<P>
+Use font 10 for residues from residues 3-20 of sequences 12-40. The font
+must have been defined using the DEFINE_FONTcommand.
+<P>
+FONT_RESIDUE <int> <int> <int>
+<P>
+Set the font for use with a single residue position - most useful when used
+with the TEXT command.
+<P>
+e.g.
+<P>
+FONT_RESIDUE 3 7 2
+<P>
+Use font 2 for residue 3 of sequence 7. Font 2 must have been defined using
+the DEFINE_FONT command.
+<P>
+LINE <string> <int> <int> <int>
+<P>
+There are four commands of this type for drawing horizontal or vertical lines
+on the alignment.
+<P>
+LINE LEFT <int> <int> <int>
+<P>
+Draw a line to the left of the character positions indicated.
+<P>
+e.g.
+<P>
+LINE LEFT 3 12 24
+<P>
+Draw a vertical line starting at residue 3 of sequence 12 and ending at
+residue 3 of sequence 24.
+<P>
+LINE TOP 3 12 24
+<P>
+Draw a horizontal line above the character positions from residue 3 of
+sequence 12 to residue 24 of sequence 12.
+<P>
+Similar commands are:
+<P>
+LINE BOTTOM <int> <int> <int> Draw a line at bottom of character position.
+<P>
+LINE RIGHT <int> <int> <int> Draw a line at right of character position.
+<P>
+BOX_REGION <int> <int> <int> <int>
+<P>
+Draw a box around the region indicated by the four integers.
+<P>
+e.g.
+<P>
+BOX_REGION 2 5 30 7
+<P>
+Would box from residue 2 of sequence 5 to residue 30 of sequence 7.
+<P>
+SHADE_REGION <int> <int> <int> <int> <float>
+<P>
+Shade the region indicated by the integers with the grey value shown by the
+float.
+e.g.
+<P>
+SHADE_REGION 30 40 35 46 0.2
+<P>
+Would shade from residue 30-35 of sequences 40-46 with a grey value of 0.2.
+<P>
+SHADE_RES <int> <int> <float>
+<P>
+Shade just one amino acid with the grey value.
+<P>
+e.g.
+<P>
+SHADE_RES 3 4 0.7
+<P>
+Shades residue 3 of sequence 7. (Note: this can also be achieved with the
+<P>
+SHADE_REGION command, but requires 2 extra numbers)
+<P>
+TEXT <int> <int> <qstring>
+<P>
+Place the text string at the location indicated.
+<P>
+e.g.
+<P>
+TEXT 30 70 "Active Site His"
+<P>
+would put the text Active Site His starting at position 30 of sequence
+70. (Use FONT_RESIDUE or FONT_REGION commands to set the font of the
+text). Text added with the TEXT command will not be split across page
+breaks, so you may in some circumstances need to fiddle a little with
+the location/pointsize for the text to get the desired result.
+<P>
+ID_FONT ALL <int>
+<P>
+Set the font for all identifier codes to the font number shown by <int>.
+e.g.
+<P>
+ID_FONT ALL 3
+<P>
+Would set all the identifier codes to font 3.
+<P>
+ID_FONT <int> <int>
+<P>
+Set the font for a specific identifier to font number.
+e.g.
+<P>
+ID_FONT 12 4
+<P>
+Use font 4 for the identifer of sequence 12, default font for all other
+identifiers.
+<P>
+SUB_CHARS ALL <char> <char>
+<P>
+Substitute the characters indicated.
+<P>
+e.g.
+<P>
+SUB_CHARS ALL + *
+<P>
+would change all occurences of + to * in the alignment.
+<P>
+SUB_CHARS <int> <int> <int> <int> <char> <char>
+<P>
+restrict the substitution to the region shown.
+<P>
+e.g.
+<P>
+SUB_CHARS 1 1 7 8 %*
+<P>
+would substitute * for %from residue 1-7 of sequences 1-8.
+NOTE: To substitute for or with the space character use the word SPACE.
+e.g. to change all space characters to -.
+<P>
+SUB_CHARS ALL SPACE -
+<P>
+SUB_ID <int> <qstring>
+<P>
+Replace the numbered identifier by the string.
+e.g.
+<P>
+SUB_ID 34 "Predicted Secondary Structure"
+<P>
+would replace whatever the identifier of sequence 34 was, by the text shown.
+This is useful when used in conjunction with the ADD_SEQ command shown under
+the STEP 1 commands.
+<P>
+INVERSE_CHARS <string> ALL/Range (similar syntax to FONT_CHARS but no
+font number)
+<P>
+Print the selected characters in white. This clearly will only work
+if you first use the SHADE_CHARScommand to shade the characters with
+something other than white.
+<P>
+CCOL_CHARS <string> ALL <int>
+<P>
+Colour all characters in the <string> by the colour defined by <int>.
+<P>
+e.g.
+<P>
+CCOL_CHARS GP ALL 12
+<P>
+would colour all G and P characters in the alignment by the colour 12.
+This colour MUST have been defined by the DEFINE_COLOUR command.
+<P>
+CCOL_CHARS <string> <int> <int> <int> <int> <int>
+<P>
+restricts the colouring to the region defined by the four integers. Thus
+<P>
+CCOL_CHARS ILVW 3 12 7 32 7
+<P>
+would colour I L V and W characters from residues 3-7 of sequences 12-32
+inclusive with the colour 7.
+<P>
+SCOL_CHARS: This has identical syntax to SCOL_CHARS, but colours the
+background of the character, rather than the letter itself.
+<P>
+COLOUR_REGION <int> <int> <int> <int> <int>
+<P>
+COLOR_REGIONColour the region indicated by the integers with the colour number given
+as the last number.
+<P>
+e.g.
+<P>
+COLOUR_REGION 30 40 35 46 2
+<P>
+Would colour from residue 30-35 of sequences 40-46 with the colour 2.
+<P>
+COLOUR_RES <int> <int> <int>
+<P>
+Colour just one amino acid with the defined colour.
+<P>
+e.g.
+<P>
+COLOUR_RES 3 4 7
+<P>
+Colours residue 3 of sequence 7. (Note: this can also be achieved with the
+COLOUR_REGION command, but requires 2 extra numbers)
+<P>
+<HR> <A NAME=tex2html393 HREF=subsection3_16_2.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/next_motif.gif"></A> <A NAME=tex2html391 HREF=subsection3_16_1.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/up_motif.gif"></A> <A NAME=tex2html387 HREF=subsubsection3_16_1_3.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/previous_motif.gif"></A> <A NAME=tex2html395 HREF=tableofcontents3_1.html><IMG ALIGN=MIDDLE SRC="http://geoff.biop.ox.ac.uk/latex2html/contents_motif.gif"></A> <BR>
+<B> Next:</B> <A NAME=tex2html394 HREF=subsection3_16_2.html> AMPS Block file </A>
+<B>Up:</B> <A NAME=tex2html392 HREF=subsection3_16_1.html> ALSCRIPT Command Summary</A>
+<B> Previous:</B> <A NAME=tex2html388 HREF=subsubsection3_16_1_3.html> OPTIONAL STEP 1 </A>
+<HR> <P>
+<HR>
+
+</BODY>
+<P><ADDRESS>
+gjb@bioch.ox.ac.uk
+</ADDRESS>
\ No newline at end of file
git://source.jalview.org / jpred.git / blobdiff